I have been searching for an "official" answer to this. At first it seems odd to me to increase the total power draw capability to 2A, but only make 600mA available to the USB ports. The closest explanation I've found so far is from a forum moderator in this thread:

If anyone has a B+ board, there is a hidden config option:

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safe_mode_gpio=4

By default the USB ports are limited to 600mA.
With the new option, this is increased to 1200mA.

Note: this was just for internal testing. In the next firmware update this will be renamed to

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max_usb_current=1

The idea is you only set this option if you know you have a good (e.g. 2A) power supply.

I guess I understand the reasoning that many people might still just have 1A power supplies, so you need to manually enable the 1200mA output if and only if you know you have a higher-rated supply. However, I can also see new users being confused when they read that the B+ can "handle more USB devices" or "draw 2 amps" and then get confused when they need to manually allow their USB ports to actually supply a lot of current, since they expect that behavior to work out-of-the-box.

Don't read anything I say as 'official', but it's because many people have terrible power supplies. When you have a 1A supply and the usb devices draw a lot of current, you can brown out the supply and cause the pi to reset or hang. If the usb current is limited, it's more likely to only take out usb devices and the pi can recover, which is more desirable. Since good 2A supplies are not the norm, it makes more sense to leave the 1.2A option for people who know what they're doing.